The initial episode of LEGO Star Wars: The Yoda Chronicles, titled "The Phantom Clone," was originally broadcast on Cartoon Network on May 29, 2013.
The Clone Wars are raging across the galaxy, creating a period of intense danger with no end in sight. A scheme devised by the Sith, spearheaded by the nefarious Palpatine and his minion Dooku, threatens to bring about the Republic's demise.
While en route to Coruscant in his Starfighter, General Grievous ambushes a pair of Z-95 Headhunters, affirming to Dooku that their strategy is unfolding flawlessly. At the Jedi Temple, Yoda demonstrates the bravery of Anakin Skywalker to Vaash Ti, Rako, Bobby, and Bene. C-3PO boasts about his connection to Anakin, but suddenly senses a disturbance and a potent threat through the Force.
Darth Sidious, via hologram, orders Grievous to commence the attack, adding sarcastically that it should occur 'a week from now.' He then transforms back into Supreme Chancellor Palpatine to inform Yoda about a distress signal purportedly sent by Obi-Wan Kenobi from Alderaan. Grievous calls back to confirm Sidious' sarcasm, prompting Sidious to instruct him to launch the attack immediately. Sidious reverts to Palpatine once more, only to realize he's still conversing with Grievous. Becoming confused and frustrated with the transformations, he abandons the effort. Yoda entrusts his Padawans to C-3PO's care and departs with Mace Windu, R2-D2, and CC-2224 aboard a Republic Gunship to rescue Obi-Wan. As they depart, Grievous infiltrates the Holocron Vault and assaults the students. The Republic Gunship approaches Alderaan, responding to Obi-Wan's supposed plea, only to discover that he never sent a distress call. Admiral Ackbar reveals the trap as Separatist ships arrive to attack.
Grievous confiscates the padawans' Lightsabers, prompting the children to launch an assault against him. As Yoda, Mace, and R2-D2 struggle to repel the invasion of Vulture Droids, Tri-Fighters, and Star Destroyers, Admiral Gial Ackbar and Cody initiate the jump to lightspeed as the gunship is split in half, leaving Mace, Yoda, and Artoo marooned in space. As Grievous makes his escape in his Starfighter, the padawans, disregarding Threepio's objections, board their school bus and attempt to locate their weapons through the Force. Bene unveils her modified engines on the bus, propelling the group into lightspeed and towards Tatooine.
Yoda and Mace crash into the murky waters of Dagobah (Artoo utilizes a parachute). As they establish a camp, the two Jedi ponder the identity of the hidden Sith Lord, completely dismissing R2-D2's suggestion that it's Palpatine. Vaash Ti and the others land on Tatooine, where Jabba the Hutt runs over C-3PO in his sail barge and is in possession of the lightsabers. The group gives chase. As R2-D2 loses hope, Lindo Calrissian and his son Lando arrive in the disco-themed Millennium Falcon and rescue the Jedi.
C-3PO knocks on the doors of Jabba's Palace and hurls insults at Bib Fortuna and Malakili, who subsequently unleash the Rancor upon him. The padawans infiltrate the palace, evade the Gamorrean Guards, and retrieve the lightsabers, which are inoperable due to the absence of the Kaiburr crystals. Bobby inadvertently awakens Jabba, but fortunately, the padawans liberate Young Han Solo from a block of carbonite and reunite with C-3PO, who rides the rancor to safety.
On Kamino, Grievous and Count Dooku utilize the Kaiburr crystals to create an immensely powerful crystal, which they intend to use to power their cloning chamber. Darth Sidious expresses his gratitude via hologram, and the Sith Clones begin to materialize. The Disco Falcon races towards Coruscant, and C-3PO contacts them through hologram, and Bobby briefs Yoda on the situation. Lindo activates the hyperdrive engine, executing a rainbow-colored jump to Lightspeed towards Kamino. As the Calrissians depart, Artoo and the Jedi break into the cloning chamber, only to be confronted by Grievous. Fortunately, Yoda uses the Force to push Grievous into a pit, and Mace engages Dooku in combat. As Dooku gains the upper hand, Yoda seizes him and hurls him at the Kaiburr crystal, disabling the cloning chamber before the clones can be activated, with the exception of one.
Jek-14 activates and begins to rebuild the palace as Yoda battles Dooku and Grievous regains consciousness and ambushes Mace. C-3PO senses that Artoo is in danger through the power of Wifi and the Padawans depart to Kamino. Outside, Grievous begins rusting in the rain and Mace rips his Blaster away from him. As Jek tortures a lightsaberless Yoda, Yoda grabs the blaster from Mace and fires at Jek, but the Sith Clone reflects them and sends the Jedi right back outside, knocking over Grievous as well. Dooku takes the crystal and begins reactivating the cloning machine as Jek prepares to finish the Jedi off. He force-chokes Yoda into unconsciousness but stops before he can kill him, which baffles everyone. Before anyone can ask, the school bus arrives and begins to detonate the cloning chamber with a giant laser cannon that Bene had added. Yoda and Mace jump on the ship, Artoo flies out of the palace with the crystal and the heroes escape the remains. Dooku and Jek hop in a Mandalorian Speeder and evacuate as the planet of Kamino collapses in a fantastic lightshow.
Back in the Holocron Vault, Yoda congratulates the padawans with his own celebratory stickers, and reveals his intentions to hunt down Jek to the last brick. On Geonosis, Dooku reveals Jek to Darth Sidious. Grievous arrives from the ocean with a life tube and the Sith celebrate their 'victory'.